Mercurial > repos > iuc > mothur_merge_taxsummary

comparison merge.taxsummary.xml @ 2:297f3f6ad488 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
author iuc
date Tue, 20 Mar 2018 22:26:37 -0400
parents 8eebcd1d81b0
children
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1:850d7a1bccc3 2:297f3f6ad488
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 #for $i in $input: 13 #for $i in $input:
14 ln -s "$i" input${input.index($i)}.dat && 14 ln -s '$i' input${input.index($i)}.dat &&
15 #end for 15 #end for
16 16
17 echo 'merge.taxsummary( 17 echo 'merge.taxsummary(
18 input=#for $i in $input#input${input.index($i)}.dat-#end for#, 18 input=#for $i in $input#input${input.index($i)}.dat-#end for#,
19 output=$output 19 output=$output
20 )' 20 )'
21 | sed 's/ //g' ## mothur trips over whitespace 21 | sed 's/ //g' ## mothur trips over whitespace
22 | sed 's/-,/,/g' 22 | sed 's/-,/,/g'
23 | mothur 23 | mothur
24 | tee mothur.out.log 24 | tee mothur.out.log
25 ]]></command> 25 ]]></command>
26 <inputs> 26 <inputs>
27 <param name="input" type="data" format="mothur.tax.summary" multiple="true" label="input - tax.summary files"/> 27 <param name="input" type="data" format="mothur.tax.summary" multiple="true" label="input - tax.summary files"/>
28 <expand macro="param-savelog"/>
28 </inputs> 29 </inputs>
29 <outputs> 30 <outputs>
30 <expand macro="logfile-output"/> 31 <expand macro="logfile-output"/>
31 <data name="output" format="mothur.tax.summary" label="${tool.name} on ${on_string}: merged sff"/> 32 <data name="output" format="mothur.tax.summary" label="${tool.name} on ${on_string}: merged sff"/>
32 </outputs> 33 </outputs>
33 <tests> 34 <tests>
34 <test> 35 <test>
35 <param name="input" value="amazon.wang.knn.tax.summary,amazon.silva.wang.tax.summary"/> 36 <param name="input" value="amazon.wang.knn.tax.summary,amazon.silva.wang.tax.summary"/>
36 <output name="output" md5="6e1276cc740b03d5407a3707322e1ee3" ftype="mothur.tax.summary"/> 37 <output name="output" md5="7175d0709a1e4622d0710e79dd52801b" ftype="mothur.tax.summary"/>
38 <param name="savelog" value="true"/>
37 <expand macro="logfile-test"/> 39 <expand macro="logfile-test"/>
38 </test> 40 </test>
39 </tests> 41 </tests>
40 <help> 42 <help><![CDATA[
41 <![CDATA[
42 43
43 @MOTHUR_OVERVIEW@ 44 @MOTHUR_OVERVIEW@
44 45
45 .. _Mothur: https://www.mothur.org/wiki/Main_Page 46 .. _Mothur: https://www.mothur.org/wiki/Main_Page
46 47
48 49
49 The merge.taxsummary command takes a list of tax.summary files separated by dashes and merges them into one file. 50 The merge.taxsummary command takes a list of tax.summary files separated by dashes and merges them into one file.
50 51
51 .. _merge.taxsummary: https://www.mothur.org/wiki/Merge.taxsummary 52 .. _merge.taxsummary: https://www.mothur.org/wiki/Merge.taxsummary
52 53
53 ]]> 54 ]]></help>
54 </help>
55 <expand macro="citations"/> 55 <expand macro="citations"/>
56 </tool> 56 </tool>